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Background: Damask roses (Rosa damascena Mill.) are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 accessions of R. damascena collected across major and minor rose oil production areas in Iran. Results: All microsatellite markers showed a high level of polymorphism (5–15 alleles per microsatellite marker, with an average of 9.11 alleles per locus). Cluster analysis of genetic similarities revealed that these microsatellites identified a total of nine different genotypes. The genotype from Isfahan province, which is the major production area, was by far the most common genotype (27/40 accessions). It was identical to the Bulgarian genotype. Other genotypes (each represented by 1–4 accessions) were collected from minor production areas in several provinces, notably in the mountainous Northwest of Iran. Conclusion: This is the first study that uncovered genetic diversity within Damask rose. Our results will guide new collection activities to establish larger collections and manage the Iranian Damask rose genetic resources. The genotypes identified here may be directly useful for breeding. Background There are almost 200 species and more than 18000 cultivars in the genus Rosa [1]. They are mostly shrubs, distributed in the temperate zones of the Northern hemisphere [2]. One of the important Rosa species is Rosa damascena Mill., which is commercially used for essential oil production and cultivated as garden rose [3]. In recent years, antioxidant, antibacterial and antimicrobial activities of R. damascena essential oil have been demonstrated [4-7]. Three recent studies on molecular analyses of genetic diversity of Rosa damascena Mill. with RAPD, AFLP and SSR markers did not show any polymorphism among R. Published: 8 March 2007 BMC Plant Biology 2007, 7:12 doi:10.1186/1471-2229-7-12 Received: 24 November 2006 Accepted: 8 March 2007 This article is available from: http://www.biomedcentral.com/1471-2229/7/12 © 2007 Babaei et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.